personal experience:
on a mountain bike we must get back-off the saddle more often therefore the saddle is usually a little lower...on LOOOOOONG climbs i will raise my saddle to ease knee issues.
since doing this my knees have stopped yelling at me...just remember to put it back down BEFORE you hit the techy downhill section!

i noticed you said you do alot of climbing...i know this method is a pain in the katoosh but your knees will thank you!!!

try this if you don't have one already:

http://www.cambriabike.com/shopexd.asp?id=26050

my $0.02